Distribution of Insertion Sequence ISRm1 in Rhizobium meliloti and Other Gram-negative Bacteria

Wheatcroft, Roger; Watson, Robert J.

doi:10.1099/00221287-134-1-113

Cited by 20 publications

(21 citation statements)

References 20 publications

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“…Recombinant plasmid DNA was prepared as previously described (34). Restriction fragments wanted for cloning or use as probes were collected from agarose gels by using NA45 paper (Schleicher and Schuell) during electrophoresis (35). Total cellular DNA was isolated from 5-ml bacterial cultures, restricted with endonucleases, and prepared for probing in Southern blots as previously described (36).…”

Section: Methodsmentioning

confidence: 99%

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Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2

Wheatcroft¹,

Laberge²

1991

J Bacteriol

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The insertion sequence ISRm3 was discovered simultaneously in different Rhizobium melioti strains by probing Southern blots of total cellular DNA with 32P-labeled pTA2. This plasmid is indigenous to strain IZ450 and fortuitously contained four copies of ISRm3. By using an internal EcoRI fragment as a specific probe (pRWRm31), homology to ISRm3 was subsequently detected in over 90% of R. melioti strains tested from different geographical locations around the world. The frequency of stable nonlethal ISRm3 transpositions was estimated to be 4 x 10-5 per generation per cell in strain SU47 when grown in liquid culture. The entire nucleotide sequence of ISRm3 in R. meliloti 102F70 is 1,298 bp and has 30-bp terminal inverted repeats which are perfectly matched. Analysis of six copies of ISRm3 in two strains showed that a variable number of base pairs (usually eight or nine) were duplicated and formed direct repeats adjacent to the site of insertion. On one DNA strand, ISRm3 contains an open reading frame spanning 93% of its length. Comparison of the putative protein encoded with sequences derived from the EMBL and GenBank databases showed significant similarity between the putative transposases of ISRm3 from R. melilodi, IS256 from Staphylococcus aureus, and IS12 from ThiobaciUlusferrooxidans. These insertion sequences appear to be distantly related members of a distinct class.

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Section: Methodsmentioning

confidence: 99%

“…IS are widely distributed among R. meliloti strains (35) and can be maintained at high copy number in natural populations (la). They can coexist in the same cell in multiple copies located on both plasmids and the chromosome (35). IS are important because of their effect upon the stability and regulation of genes (12,15).…”

mentioning

confidence: 99%

Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2

Wheatcroft¹,

Laberge²

1991

J Bacteriol

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“…In R. meliloti, ISRm1 is present in 1 to 11 copies (53) and, like ISRm2, is preferentially found in association with symbiotic genes (15,44). Other elements such as ISRm3, ISRm4, and ISRm5 were also characterized (30,48,54), suggesting that most R. meliloti strains carry over 50 IS copies per genome (30).…”

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confidence: 99%

Structure and evolution of NGRRS-1, a complex, repeated element in the genome of Rhizobium sp. strain NGR234

et al. 1997

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Much of the remarkable ability of Rhizobium sp. strain NGR234 to nodulate at least 110 genera of legumes, as well as the nonlegume Parasponia andersonii, stems from the more than 80 different Nod factors it secretes. Except for nodE, nodG, and nodPQ, which are on the chromosome, most Nod factor biosynthesis genes are dispersed over the 536,165-bp symbiotic plasmid, pNGR234a. Mosaic sequences and insertion sequences (ISs) comprise 18% of pNGR234a. Many of them are clustered, and these IS islands divide the replicon into large blocks of functionally related genes. At 6 kb, NGRRS-1 is a striking example: there is one copy on pNGR234a and three others on the chromosome. DNA sequence comparisons of two NGRRS-1 elements identified three types of IS, NGRIS-2, NGRIS-4, and NGRIS-10. Here we show that all four copies of NGRRS-1 probably originated from transposition of NGRIS-4 into a more ancient IS-like sequence, NGRIS-10. Remarkably, all nine copies of NGRIS-4 have transposed into other ISs. It is unclear whether the accumulation of potentially mutagenic sequences in large clusters is due to the nature of the IS involved or to some selection process. Nevertheless, a direct consequence of the preferential targeting of transposons into such IS islands is to minimize the likelihood of disrupting vital functions.

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“…In Rhizobium meliloti, several mutations affecting symbiotic nitrogen fixation with alfalfa (Medicago sativa) have been shown to be the result of spontaneous IS transposition (10,29,33,48). More than 25 distinct IS elements have been found in this species, and it is common for several to occupy the same genome in multiple copies (39,50). We estimate that most R. meliloti strains carry more than 50 IS copies in total, which, if active in transposition, would be expected to have a considerable effect upon genetic stability.…”

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confidence: 99%

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

Laberge¹,

Middleton²,

Wheatcroft³

1995

J Bacteriol

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A target for ISRm3 transposition in Rhizobium meliloti IZ450 is another insertion sequence element, named ISRm5. ISRm5 is 1,340 bp in length and possesses terminal inverted repeats of unequal lengths (27 and 28 bp) and contain five mismatches. An open reading frame that spans 89% of the length of one DNA strand encodes a putative transposase with significant similarity to the putative transposases of 11 insertion sequence elements from diverse bacterial species, including ISRm3 from R. meliloti. Multiple copies and variants of ISRm5 occur in the R. meliloti genome, often in close association with ISRm3. Five ISRm5 copies in two strains were studied, and each was found to be located between 8-bp direct repeats. At two of these loci, which were shown to be highly conserved in R. meliloti, the copies of ISRm5 were found to be associated with pairs of short inverted repeats resembling transcription terminators. This structural arrangement not only may provide a conserved niche for ISRm5 but also may be a preferred target for transposition.Insertion sequences (IS) are small transposable elements of DNA that are widespread in bacteria (see references 15 and 16 for reviews). They are responsible for various types of genomic modification, including DNA rearrangement, deletion, and duplication. By transposition, they cause insertional mutations which may disrupt genes or modify their transcription. In Rhizobium meliloti, several mutations affecting symbiotic nitrogen fixation with alfalfa (Medicago sativa) have been shown to be the result of spontaneous IS transposition (10,29,33,48). More than 25 distinct IS elements have been found in this species, and it is common for several to occupy the same genome in multiple copies (39, 50). We estimate that most R. meliloti strains carry more than 50 IS copies in total, which, if active in transposition, would be expected to have a considerable effect upon genetic stability. This is consistent with the wide genotypic and phenotypic diversity found within the species generally (11) and in field populations (20,22). As yet, few detailed studies of the IS elements of R. meliloti have been made beyond their distributions and copy numbers. However, it is already clear that there are significant differences in their primary structures and transposition behaviors (10,41,46,47).In this paper, we report the discovery, characterization, and full nucleotide sequence of ISRm5 from R. meliloti IZ450. We describe the structural similarity of two ISRm5-containing loci that are highly conserved in the species. We show that ISRm5 is a target for insertion by ISRm3 (47) and that these IS elements are often closely associated in the R. meliloti genome. ISRm3 and ISRm5 are shown to be structurally distinct elements yet to be related by the similarity of the transposases that they putatively encode. MATERIALS AND METHODSPlasmids, strains, and growth conditions. The bacterial strains and plasmids used in this study are listed in Table 1. R. meliloti and Agrobacterium radiobacter were grown in TY med...

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Distribution of Insertion Sequence ISRm1 in Rhizobium meliloti and Other Gram-negative Bacteria

Cited by 20 publications

References 20 publications

Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2

Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2

Structure and evolution of NGRRS-1, a complex, repeated element in the genome of Rhizobium sp. strain NGR234

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

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